significant common variant, and recombination must increase to 5×10−3 to reduce the proportion to below 1%. Importantly, the simulations involving recombination prohibit evaluation of any common variant that has a rare causal site within the same segment. Thus the synthetic associations emerging in these simulations occur between sites that are separated by a minimum recombination distance of that between segments, which is 1×10−3 to 5×10−3. It is counterintuitive that recombination would increase synthetic associations since recombination reduces the average LD in a region. The observation can be explained, however, by the effect of recombination on the distribution of association amongst sites within a genomic region. Although the average LD declines as recombination increases, it is not known how higher moments behave and these moments can influence the proportion of pairs of sites that exceed some given threshold level of association.
